rs11682718

Variant names:

• chr2-66821029-G-A
• rs11682718
• ENST00000455096.1:n.1220C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000455096.1(DNMT3AP1):​n.1220C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 154,702 control chromosomes in the GnomAD database, including 601 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.073 (597 hom., cov: 32)
  • Exomes 𝑓: 0.055 (4 hom.)
• Consequence: DNMT3AP1 ENST00000455096.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.92
• Publications: 1 publications found

Genes affected

DNMT3AP1 (HGNC:23164): (DNA methyltransferase 3A pseudogene 1)

LINC01798 (HGNC:52588): (long intergenic non-protein coding RNA 1798)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455096.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNMT3AP1	ENST00000455096.1	TSL:6	n.1220C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC01798	ENST00000715601.1		n.185-26957G>A		intron	N/A
	LINC01798	ENST00000758432.1		n.185-26957G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11072 AN: 152102 Hom.: 595 Cov.: 32

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0694

GnomAD4 exome AF: 0.0548 AC: 136 AN: 2482 Hom.: 4 Cov.: 0 AF XY: 0.0540 AC XY: 71 AN XY: 1316

African (AFR) AF: 0.00 AC: 0 AN: 20

American (AMR) AF: 0.150 AC: 3 AN: 20

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22

East Asian (EAS) AF: 0.0556 AC: 1 AN: 18

South Asian (SAS) AF: 0.0437 AC: 9 AN: 206

European-Finnish (FIN) AF: 0.0543 AC: 38 AN: 700

Middle Eastern (MID) AF: 0.0214 AC: 6 AN: 280

European-Non Finnish (NFE) AF: 0.0672 AC: 74 AN: 1102

Other (OTH) AF: 0.0439 AC: 5 AN: 114

GnomAD4 genome AF: 0.0728 AC: 11077 AN: 152220 Hom.: 597 Cov.: 32 AF XY: 0.0758 AC XY: 5638 AN XY: 74428

African (AFR) AF: 0.0165 AC: 687 AN: 41556

American (AMR) AF: 0.148 AC: 2268 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.0813 AC: 421 AN: 5176

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1086 AN: 10592

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5905 AN: 67996

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0785 Hom.: 949

Bravo AF: 0.0711

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.5
DANN	Benign	0.65
PhyloP100		2.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11682718;

hg19: chr2-67048161;